bioconductor.org "Spatial" keyword
SpatialFeatureExperiment 1.14.0
Integrating SpatialExperiment with Simple Features in sf14 versions - Latest release: about 10 hours ago - 1 dependent package - 19.4 thousand downloads total - 57 stars on GitHub - 1 maintainer
tomoseqr 1.16.0
R Package for Analyzing Tomo-seq Data7 versions - Latest release: about 21 hours ago - 8.79 thousand downloads total - 1 maintainer
clustSIGNAL 1.4.0
ClustSIGNAL: a spatial clustering method3 versions - Latest release: 2 days ago - 3.53 thousand downloads total - 6 stars on GitHub - 1 maintainer
imcRtools 1.18.0
Methods for imaging mass cytometry data analysis7 versions - Latest release: 3 days ago - 1 dependent package - 22.9 thousand downloads total - 27 stars on GitHub - 1 maintainer
BulkSignalR 1.4.0
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...7 versions - Latest release: 4 days ago - 6.86 thousand downloads total - 1 stars on GitHub - 1 maintainer
betaHMM 1.8.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...7 versions - Latest release: 5 days ago - 6.11 thousand downloads total - 1 maintainer
Banksy 1.8.1
Spatial transcriptomic clustering5 versions - Latest release: 6 days ago - 17 thousand downloads total - 123 stars on GitHub - 1 maintainer
spARI 1.2.0
Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering2 versions - Latest release: 6 days ago - 1.77 thousand downloads total - 1 maintainer
FuseSOM 1.14.0
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets7 versions - Latest release: 8 days ago - 8.86 thousand downloads total - 1 stars on GitHub - 1 maintainer
GeomxTools 3.16.0
NanoString GeoMx Tools10 versions - Latest release: 8 days ago - 3 dependent packages - 39.4 thousand downloads total - 1 maintainer
scider 1.10.0
Spatial cell-type inter-correlation by density in R6 versions - Latest release: 8 days ago - 7.64 thousand downloads total - 7 stars on GitHub - 1 maintainer
concordexR 1.12.0
Identify Spatial Homogeneous Regions with concordex7 versions - Latest release: 9 days ago - 8.26 thousand downloads total - 10 stars on GitHub - 1 maintainer
spicyR 1.24.0
Spatial analysis of in situ cytometry data14 versions - Latest release: 9 days ago - 2 dependent packages - 21.8 thousand downloads total - 10 stars on GitHub - 1 maintainer
CTSV 1.14.0
Identification of cell-type-specific spatially variable genes accounting for excess zeros7 versions - Latest release: 9 days ago - 8.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
spatialHeatmap 2.18.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions17 versions - Latest release: 9 days ago - 15.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
stJoincount 1.13.0
stJoincount - Join count statistic for quantifying spatial correlation between clusters7 versions - Latest release: 9 days ago - 8.59 thousand downloads total - 5 stars on GitHub - 1 maintainer
alabaster.sfe 1.4.0
Language agnostic on disk serialization of SpatialFeatureExperiment3 versions - Latest release: 9 days ago - 2.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
Voyager 1.14.0
From geospatial to spatial omics7 versions - Latest release: 10 days ago - 14 thousand downloads total - 96 stars on GitHub - 1 maintainer
SPIAT 1.14.0
Spatial Image Analysis of Tissues12 versions - Latest release: 10 days ago - 12.6 thousand downloads total - 24 stars on GitHub - 1 maintainer
ggspavis 1.18.0
Visualization functions for spatial transcriptomics data11 versions - Latest release: 10 days ago - 1 dependent package - 19.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
visiumStitched 1.4.0
Enable downstream analysis of Visium capture areas stitched together with Fiji3 versions - Latest release: 10 days ago - 3.92 thousand downloads total - 4 stars on GitHub - 1 maintainer
smoothclust 1.8.0
smoothclust7 versions - Latest release: 10 days ago - 5.89 thousand downloads total - 1 stars on GitHub - 1 maintainer
miRspongeR 2.16.0
Identification and analysis of miRNA sponge regulation9 versions - Latest release: 11 days ago - 1 dependent package - 13.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
8 versions - Latest release: 11 days ago - 36 dependent packages - 361 thousand downloads total - 54 stars on GitHub - 1 maintainer
SpatialExperiment 1.22.0
S4 Class for Spatially Resolved -omics Data8 versions - Latest release: 11 days ago - 36 dependent packages - 361 thousand downloads total - 54 stars on GitHub - 1 maintainer
ggsc 1.10.0
Visualizing Single Cell and Spatial Transcriptomics8 versions - Latest release: 12 days ago - 8.67 thousand downloads total - 30 stars on GitHub - 1 maintainer
SEraster 1.4.0
Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis3 versions - Latest release: 12 days ago - 3.42 thousand downloads total - 19 stars on GitHub - 1 maintainer
signifinder 1.13.0
Collection and implementation of public transcriptional cancer signatures8 versions - Latest release: 12 days ago - 7.57 thousand downloads total - 9 stars on GitHub - 1 maintainer
pengls 1.18.0
Fit Penalised Generalised Least Squares models7 versions - Latest release: 12 days ago - 8.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpatialOmicsOverlay 1.12.0
Spatial Overlay for Omic Data from Nanostring GeoMx Data8 versions - Latest release: 13 days ago - 8.44 thousand downloads total - 1 maintainer
nnSVG 1.16.0
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data11 versions - Latest release: 13 days ago - 2 dependent packages - 13.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
scatterHatch 1.18.0
Creates hatched patterns for scatterplots7 versions - Latest release: 13 days ago - 8.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
HiCPotts 1.2.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C2 versions - Latest release: 13 days ago - 1.86 thousand downloads total - 0 stars on GitHub - 1 maintainer
mitology 1.4.0
Study of mitochondrial activity from RNA-seq data3 versions - Latest release: 13 days ago - 3.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
MoleculeExperiment 1.12.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data10 versions - Latest release: 13 days ago - 8.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
tpSVG 1.8.0
Thin plate models to detect spatially variable genes6 versions - Latest release: 14 days ago - 5.74 thousand downloads total - 2 stars on GitHub - 1 maintainer
OSTA.data 1.4.0
OSTA book data3 versions - Latest release: 14 days ago - 4.75 thousand downloads total - 2 stars on GitHub - 1 maintainer
BatchSVG 1.4.0
Identify Batch-Biased Spatially Variable Genes3 versions - Latest release: 15 days ago - 3.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
SVP 1.4.0
Predicting cell states and their variability in single-cell or spatial omics data5 versions - Latest release: 15 days ago - 4.47 thousand downloads total - 12 stars on GitHub - 1 maintainer
jazzPanda 1.4.0
Finding spatially relevant marker genes in image based spatial transcriptomics data5 versions - Latest release: 16 days ago - 4.01 thousand downloads total - 0 stars on GitHub - 1 maintainer
HuBMAPR 1.6.0
Interface to 'HuBMAP'8 versions - Latest release: 18 days ago - 4.55 thousand downloads total - 3 stars on GitHub - 1 maintainer
stPipe 1.2.0
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics3 versions - Latest release: 19 days ago - 1.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
tidySpatialExperiment 1.8.0
SpatialExperiment with tidy principles9 versions - Latest release: 19 days ago - 7.44 thousand downloads total - 8 stars on GitHub - 1 maintainer
CatsCradle 1.6.0
This package provides methods for analysing spatial transcriptomics data and for discovering gene...6 versions - Latest release: 19 days ago - 4.95 thousand downloads total - 3 stars on GitHub - 1 maintainer
standR 1.16.0
Spatial transcriptome analyses of Nanostring's DSP data in R7 versions - Latest release: 21 days ago - 13.6 thousand downloads total - 22 stars on GitHub - 1 maintainer
simpleSeg 1.14.0
A package to perform simple cell segmentation11 versions - Latest release: 21 days ago - 10.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
RankMap 1.0.0
Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell ...1 version - Latest release: 21 days ago - 35 downloads total - 1 maintainer
SpatialArtifacts 1.0.0
Identification and Classification of Spatial Artifacts in Visium and Visium HD Data1 version - Latest release: 21 days ago - 106 downloads total - 1 maintainer
SpNeigh 1.0.0
Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics1 version - Latest release: 21 days ago - 181 downloads total - 1 maintainer
DenoIST 1.0.0
DenoIST: Denoising Image-based Spatial Transcriptomics data1 version - Latest release: 21 days ago - 427 downloads total - 1 maintainer
HistoImagePlot 1.0.0
Plotting functionality for Histopathology pipeline datasets1 version - Latest release: 21 days ago - 82 downloads total - 1 maintainer
Battlefield 1.0.0
Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data1 version - Latest release: 21 days ago - 102 downloads total - 1 maintainer
HiSpaR 1.0.0
Hierarchical Inference of Spatial Positions from Hi-C Data1 version - Latest release: 21 days ago - 198 downloads total - 1 maintainer
spoon 1.6.0
Address the Mean-variance Relationship in Spatial Transcriptomics Data5 versions - Latest release: 6 months ago - 5.39 thousand downloads total - 0 stars on GitHub - 1 maintainer
shinyDSP 1.2.0
A Shiny App For Visualizing Nanostring GeoMx DSP Data3 versions - Latest release: 6 months ago - 3.65 thousand downloads total - 1 stars on GitHub - 1 maintainer
poem 1.2.0
POpulation-based Evaluation Metrics3 versions - Latest release: 6 months ago - 3.22 thousand downloads total - 11 stars on GitHub - 1 maintainer
SpatialDecon 1.20.1
Deconvolution of mixed cells from spatial and/or bulk gene expression data8 versions - Latest release: 3 months ago - 1 dependent package - 19.6 thousand downloads total - 27 stars on GitHub - 1 maintainer
mistyR 1.18.0
Multiview Intercellular SpaTial modeling framework7 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 44 stars on GitHub - 1 maintainer
SPOTlight 1.14.0
`SPOTlight`: Spatial Transcriptomics Deconvolution10 versions - Latest release: 6 months ago - 21 thousand downloads total - 203 stars on GitHub - 1 maintainer
spatialSimGP 1.4.0
Simulate Spatial Transcriptomics Data with the Mean-variance Relationship3 versions - Latest release: 6 months ago - 3.72 thousand downloads total - 0 stars on GitHub - 1 maintainer
Statial 1.12.0
A package to identify changes in cell state relative to spatial associations10 versions - Latest release: 6 months ago - 9.76 thousand downloads total - 6 stars on GitHub - 1 maintainer
scDesign3 1.8.0
A unified framework of realistic in silico data generation and statistical model inference for si...6 versions - Latest release: 6 months ago - 7.47 thousand downloads total - 115 stars on GitHub - 1 maintainer
SpaNorm 1.4.0
Spatially-aware normalisation for spatial transcriptomics data3 versions - Latest release: 6 months ago - 4.82 thousand downloads total - 17 stars on GitHub - 1 maintainer
SpaceMarkers 2.0.0
Spatial Interaction Markers4 versions - Latest release: 6 months ago - 5.47 thousand downloads total - 5 stars on GitHub - 1 maintainer
CARDspa 1.2.1
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics3 versions - Latest release: 3 months ago - 4.27 thousand downloads total - 0 stars on GitHub - 1 maintainer
retrofit 1.10.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics6 versions - Latest release: 6 months ago - 6.93 thousand downloads total - 3 stars on GitHub - 1 maintainer
knowYourCG 1.6.3
Functional analysis of DNA methylome datasets7 versions - Latest release: 4 months ago - 6.45 thousand downloads total - 7 stars on GitHub - 1 maintainer
smoppix 1.2.3
Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index5 versions - Latest release: 2 months ago - 3.89 thousand downloads total - 1 stars on GitHub - 1 maintainer
DESpace 2.2.2
DESpace: a framework to discover spatially variable genes and differential spatial patterns acros...8 versions - Latest release: 5 months ago - 9.04 thousand downloads total - 6 stars on GitHub - 1 maintainer
SpaceTrooper 1.0.1
SpaceTrooper performs Quality Control analysis of Image-Based spatial2 versions - Latest release: 4 months ago - 2.53 thousand downloads total - 8 stars on GitHub - 1 maintainer
spacexr 1.2.0
SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics2 versions - Latest release: 6 months ago - 7.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
SpatialExperimentIO 1.2.0
Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object2 versions - Latest release: 6 months ago - 4.66 thousand downloads total - 16 stars on GitHub - 1 maintainer
spatialFDA 1.2.1
A Tool for Spatial Multi-sample Comparisons3 versions - Latest release: 28 days ago - 4.15 thousand downloads total - 4 stars on GitHub - 1 maintainer
tomoda 1.20.0
Tomo-seq data analysis6 versions - Latest release: 6 months ago - 9.82 thousand downloads total - 0 stars on GitHub - 1 maintainer
scFeatures 1.10.9
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome predic...8 versions - Latest release: 3 months ago - 7.66 thousand downloads total - 14 stars on GitHub - 1 maintainer
spaSim 1.12.0
Spatial point data simulator for tissue images6 versions - Latest release: 6 months ago - 8.01 thousand downloads total - 2 stars on GitHub - 1 maintainer
VisiumIO 1.6.3
Import Visium data from the 10X Space Ranger pipeline6 versions - Latest release: 6 months ago - 8.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
sosta 1.2.0
A package for the analysis of anatomical tissue structures in spatial omics data3 versions - Latest release: 6 months ago - 4.13 thousand downloads total - 4 stars on GitHub - 1 maintainer
sccomp 2.2.0
Differential Composition and Variability Analysis for Single-Cell Data6 versions - Latest release: 6 months ago - 11.6 thousand downloads total - 112 stars on GitHub - 1 maintainer
XeniumIO 1.2.0
Import and represent Xenium data from the 10X Xenium Analyzer2 versions - Latest release: 6 months ago - 3.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpotSweeper 1.6.0
Spatially-aware quality control for spatial transcriptomics8 versions - Latest release: 6 months ago - 7.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
lisaClust 1.18.0
lisaClust: Clustering of Local Indicators of Spatial Association8 versions - Latest release: 6 months ago - 1 dependent package - 15.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
cytoviewer 1.10.0
An interactive multi-channel image viewer for R6 versions - Latest release: 6 months ago - 9 thousand downloads total - 7 stars on GitHub - 1 maintainer
escheR 1.10.0
Unified multi-dimensional visualizations with Gestalt principles7 versions - Latest release: 6 months ago - 2 dependent packages - 9.81 thousand downloads total - 7 stars on GitHub - 1 maintainer
SpotClean 1.12.1
SpotClean adjusts for spot swapping in spatial transcriptomics data9 versions - Latest release: 3 months ago - 10.3 thousand downloads total - 34 stars on GitHub - 1 maintainer
hoodscanR 1.2.0
Spatial cellular neighbourhood scanning in R2 versions - Latest release: about 2 years ago - 2.42 thousand downloads total - 9 stars on GitHub - 1 maintainer
RegionalST 1.8.0
Investigating regions of interest and performing regional cell type-specific analysis with spatia...7 versions - Latest release: 6 months ago - 5.59 thousand downloads total - 1 maintainer
STdeconvolve 1.12.0 removed
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data5 versions - Latest release: about 1 year ago - 7.67 thousand downloads total - 1 maintainer
Related Keywords
Software
87
Transcriptomics
57
SingleCell
52
GeneExpression
46
Visualization
20
DataImport
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RNASeq
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Clustering
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Sequencing
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ImmunoOncology
10
Infrastructure
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Preprocessing
8
QualityControl
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StatisticalMethod
8
DataRepresentation
8
spatial-transcriptomics
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Regression
7
CellBasedAssays
7
DifferentialExpression
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BiomedicalInformatics
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r
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DimensionReduction
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Transcription
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CellBiology
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bioconductor
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rstats
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Classification
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Microarray
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single-cell
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GeneTarget
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bioconductor-package
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spatial-omics
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Normalization
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spatial
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GraphAndNetwork
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Epigenetics
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GenomeAnnotation
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r-package
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spatial-statistics
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Network
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u24ca289073
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genomics
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visualization
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HiddenMarkovModel
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MethylationArray
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ExperimentHubSoftware
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ProprietaryPlatforms
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SequenceMatching
1
HiC
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rstudio
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hubmap
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client
1
ShinyApps
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ThirdPartyClient
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Annotation
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rna-seq
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multidimensional
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shiny
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random-effects
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multilevel
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microbiome
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